Package architecture

The package separates the physical model, retrieval, and measurement workflow. The GUI calls the workflow layer; scripts and saved sessions can use that layer without opening a window.

Area	Main responsibilities	Reference
Core physics	Grids, transforms, pulse construction, interactions, propagation, focusing, and collection	Core physics API
Retrieval	Solver selection, objectives, optimisation, progress, and result assembly	Retrieval API
Workflow	Loading, preprocessing, post-processing, uncertainty, persistence, and session replay	Workflow API
Plotting	Plot data and visualisation of traces, fields, and diagnostics	Plotting API
JAX calculations	Differentiable forward models, residuals, and pulse parameterisation	JAX API

Keep physical calculations independent of GUI state and file I/O. Prefer the shared workflow operations when adding a command or GUI control so that the same settings retain the same meaning in scripts and saved sessions.

The forward-model chapter explains the physics; retrieval and numerical methods explains the objectives and derivatives.